Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 7025148 Shewana3_2311 alpha amylase, catalytic region (RefSeq)
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__ANA3:7025148 Length = 540 Score = 643 bits (1659), Expect = 0.0 Identities = 298/529 (56%), Positives = 376/529 (71%), Gaps = 3/529 (0%) Query: 5 MMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFG 64 + WWRG VIYQIYPRS LD+ GDGVGDL GI KLDY+ASLNVD IW+SPFF SPM DFG Sbjct: 4 LTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFG 63 Query: 65 YDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPK 124 YD+SDYR+VDP+FGT++DF L+EKAH G+KV+IDQV+SHTSDQH WF ESR++RTNPK Sbjct: 64 YDISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRTNPK 123 Query: 125 ADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQ 184 ADW+VWA+PK DGT PNNWL+IFGG AW ++ RRQQYYLHNFL SQPD+NFH+P+ RQA Sbjct: 124 ADWYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAV 183 Query: 185 LDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDL 244 LDN+ FWL GVDGFRLD + F +HD +LRDNPP PK + + G E NPY +Q H Y+ Sbjct: 184 LDNVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHYYNN 243 Query: 245 SRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH 304 RP+ + F+++LR L++ YPG T+GE+ ++ L MA YT G D+LHMAY+F+LL + Sbjct: 244 DRPQTILFIEELRQLINRYPGAVTLGEVSAEDSLAVMAAYTKGEDRLHMAYSFELLTDDY 303 Query: 305 SASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGS 364 SA+Y+R+ +E + GD WPCWA NHD R A+RWG + K++ A++ SLRGS Sbjct: 304 SAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGRGKQTSDMVKMLNAMVNSLRGS 363 Query: 365 VCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGFSPVEPW 423 VC YQGEELGL EA + + +QDP+GK WP FKGRDGCRTPMPW + + GFS V PW Sbjct: 364 VCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFSGFSQVTPW 423 Query: 424 LPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQK 483 LP+ H LAV Q+ D + L+ R LA+R+ +PAL +G++ +D + LL F R Sbjct: 424 LPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEPLLVFVRTS 483 Query: 484 GDETLLCVFNLTGQEQQTTLPVEVASDLPVAH--FTATRDGSTLTLPAY 530 G++ LL FNL EQ +L H TA R TLT AY Sbjct: 484 GEQKLLVCFNLQDTEQALSLDALSIQQEITGHGLKTAQRIADTLTFSAY 532 Lambda K H 0.320 0.138 0.443 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 946 Number of extensions: 40 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 538 Length of database: 540 Length adjustment: 35 Effective length of query: 503 Effective length of database: 505 Effective search space: 254015 Effective search space used: 254015 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory